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EP2970435B1 - Verfahren zur herstellung von fabs und bispezifischen antikörpern - Google Patents

Verfahren zur herstellung von fabs und bispezifischen antikörpern Download PDF

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Publication number
EP2970435B1
EP2970435B1 EP14719931.9A EP14719931A EP2970435B1 EP 2970435 B1 EP2970435 B1 EP 2970435B1 EP 14719931 A EP14719931 A EP 14719931A EP 2970435 B1 EP2970435 B1 EP 2970435B1
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residue
light chain
heavy chain
domain
chain variable
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French (fr)
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EP2970435A1 (de
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Stephen J. Demarest
Brian Arthur KUHLMAN
Steven Morgan LEWIS
Raheleh TOUGHIRI
Xiufeng Wu
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University of North Carolina at Chapel Hill
Eli Lilly and Co
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University of North Carolina at Chapel Hill
Eli Lilly and Co
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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/46—Hybrid immunoglobulins
    • C07K16/468—Immunoglobulins having two or more different antigen binding sites, e.g. multifunctional antibodies
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/18—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans
    • C07K16/28—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
    • C07K16/2863—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants against receptors for growth factors, growth regulators
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/18—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans
    • C07K16/32—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against translation products of oncogenes
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/30—Immunoglobulins specific features characterized by aspects of specificity or valency
    • C07K2317/31—Immunoglobulins specific features characterized by aspects of specificity or valency multispecific
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/40—Immunoglobulins specific features characterized by post-translational modification
    • C07K2317/41—Glycosylation, sialylation, or fucosylation
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/50—Immunoglobulins specific features characterized by immunoglobulin fragments
    • C07K2317/515—Complete light chain, i.e. VL + CL
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/50—Immunoglobulins specific features characterized by immunoglobulin fragments
    • C07K2317/52—Constant or Fc region; Isotype
    • C07K2317/522—CH1 domain
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/50—Immunoglobulins specific features characterized by immunoglobulin fragments
    • C07K2317/52—Constant or Fc region; Isotype
    • C07K2317/524—CH2 domain
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/50—Immunoglobulins specific features characterized by immunoglobulin fragments
    • C07K2317/52—Constant or Fc region; Isotype
    • C07K2317/526—CH3 domain
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/50—Immunoglobulins specific features characterized by immunoglobulin fragments
    • C07K2317/55—Fab or Fab'
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/50—Immunoglobulins specific features characterized by immunoglobulin fragments
    • C07K2317/56—Immunoglobulins specific features characterized by immunoglobulin fragments variable (Fv) region, i.e. VH and/or VL
    • C07K2317/567—Framework region [FR]
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/60—Immunoglobulins specific features characterized by non-natural combinations of immunoglobulin fragments
    • C07K2317/64—Immunoglobulins specific features characterized by non-natural combinations of immunoglobulin fragments comprising a combination of variable region and constant region components
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/90—Immunoglobulins specific features characterized by (pharmaco)kinetic aspects or by stability of the immunoglobulin
    • C07K2317/92—Affinity (KD), association rate (Ka), dissociation rate (Kd) or EC50 value
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/90—Immunoglobulins specific features characterized by (pharmaco)kinetic aspects or by stability of the immunoglobulin
    • C07K2317/94—Stability, e.g. half-life, pH, temperature or enzyme-resistance

Definitions

  • Antibody therapies represent an ever increasing segment of the global pharmaceutical market. Approved antibody-based products include treatments for cancer, rheumatoid arthritis, infectious diseases, cardiovascular disease and autoimmune disorders. However, to improve patient outcomes, co-administration of two or more agents that perturb distinct therapeutic targets or biochemical pathways is often desired. In this context, antibody therapy has limitations.
  • Co-administration of two or more antibody therapies requires multiple injections or, alternatively, a single injection of a co-formulation of two different antibody compositions. While multiple injections permit flexibility in dose and timing of administration, the inconvenience and discomfort associated with multiple injections may reduce patient compliance. On the other hand, while a co-formulation of multiple antibody agents would permit fewer injections, the difficulty and/or expense associated with designing a suitable pharmaceutical formulation that provides the necessary stability and bioavailability, for each antibody ingredient, may be prohibitive. Furthermore, any treatment regime which entails administration of separate antibody agents will incur the added manufacturing and regulatory cost associated with the development of each individual agent.
  • the archetypical antibody is comprised of two identical antigen binding fragments (Fabs) which not only direct binding to a particular antigenic determinant, but also provide the interface for assembly between heavy chain (HC)-light chain (LC) pairs.
  • Fabs antigen binding fragments
  • Bispecific antibodies - single agents capable of binding to two distinct antigens - have been proposed as a means for addressing the limitations attendant with co-administration or co-formulation of separate antibody agents.
  • Bispecific antibodies may integrate the binding activity of two separate MAb therapeutics, providing a cost and convenience benefit to the patient. Under certain circumstances, bispecific antibodies may elicit synergistic or novel activities beyond what an antibody combination can achieve.
  • One example of novel activity provided by bispecific antibodies would be the bridging of two different cell types through the binding of distinct cell surface receptors. Alternately, bispecific antibodies could cross-link two receptors on the surface of the same cell leading to novel agonistic/antagonistic mechanisms.
  • HC variable and constant domains are recombined with the HC CH2 and CH3 domain such that the expressed chain is chimeric.
  • the HC variable and constant (CHI) domains are expressed separately (like a native LC), which results in a Fab domain with the same native sequences but with the position of the HC and LC pairs being reversed.
  • WO 2007/109254 A2 disclose a population of stabilized scFv molecules, wherein the stabilized scFv molecules comprise (i) a scFv linker interposed between a VH domain and a VL domain, wherein the VH and VL domains are linked by a disulfide bond between an amino acid in the VH domain and an amino acid in the VL domain, and wherein the VH and VL domains of the scFv molecules have Tm values of greater than 55°C or (ii) a scFv linker interposed between a VH domain and a VL domain, wherein the VH and VL domains are linked by a disulfide bond between an amino acid in the VH and an amino acid in the VL domain, and wherein scFv molecules have a Tso of greater than 49°C.
  • Rudikoff et al (PNAS, Vol. 79, pages 1979-1983, 1982 ) describe the isolation and characterization of structural and functional properties of a variant of a parental binding protein S107.
  • the variant contained a single amino acid substitution of a glutamic acid with alanine at residue 35 of HCDR1 (numbered according to Kabat).
  • the variant does not bind phosphocholine attached to carrier or as free hapten in solution but does retain antigenic determinants (idiotypes) of the parent.
  • glutamic acid-35 provides a hydrogen bond to tyrosine-94 of the light chain that appears to be critical for stability of this portion of the binding site.
  • Salfeld J G (Nature Biotechnology, Vol. 25, No. 12, pages 1369-72, 2007 ) provides a review of properties of various antibody isotypes that should be considered when developing therapeutic antibodies.
  • the methods of the present invention achieve improved specificity and, or stability in assembly of particular Fabs. Even more particular, the methods of the present invention allow the binding specificities and binding activities of the variable regions of two distinct therapeutic antibodies to be combined in a single bi-specific antibody compound.
  • the present invention provides a method for producing a first and second fragment, antigen binding (Fab) comprising: (1) co-expressing a first nucleic acid, a second nucleic acid, a third nucleic acid and a fourth nucleic acid in a host cell, wherein: (a) the first nucleic acid encodes both a first heavy chain variable domain and a first IgG heavy chain constant CH1 domain, wherein said first heavy chain variable domain comprises a lysine at residue 39 (39K) and a glutamic acid at the residue which is four amino acids upstream of the first residue of HFR3 according to Kabat, and said first IgG heavy chain constant CH1 domain comprises an alanine or arginine at residue 172 (172A) and a glycine at residue 174 (174G); (b) the second nucleic acid encodes both a first light chain variable domain and a first light chain constant domain, wherein said first light chain variable domain is a kappa isotype and comprises an arginine
  • the present invention provides a method comprising one or more of the following: said first nucleic acid encodes a heavy chain CH1 constant domain further comprising a methionine or isoleucine at residue 190 (190M or 190I); said second nucleic acid encodes a light chain constant domain further comprising an leucine at residue 133 (133L); said second nucleic acid encodes a light chain constant domain further comprising a glutamine or aspartic acid at residue 174 (174Q or 174D), and said third nucleic acid encodes a heavy chain variable domain further comprising an arginine at residue 105 (105R) with said fourth nucleic acid encoding a light chain variable domain further comprising an aspartic acid at residue 42 (42D).
  • the present invention also provides a method for producing a bispecific antibody comprising: (1) co-expressing a first nucleic acid, a second nucleic acid, a third nucleic acid and a fourth nucleic acid in a host cell: (a) the first nucleic acid encodes a first IgG heavy chain, wherein said first heavy chain comprises a variable domain comprising a lysine at residue 39 (39K) and a glutamic acid at the residue which is four amino acids upstream of the first residue of HFR3 according to Kabat, and a CH1 constant domain comprising an alanine or arginine at residue 172 (172A) and a glycine at residue 174 (174G); (b) the second nucleic acid encodes a first light chain, wherein said first light chain comprises a kappa variable domain comprising an arginine at residue 1(1R) and an aspartic acid at residue 38 (38D), and a constant domain comprising a tyrosine at residue 135
  • the present invention provides a method comprising one or more of the following: said first nucleic acid encodes a heavy chain CH1 constant domain further comprising a methionine or isoleucine at residue 190 (190M or 190I); said second nucleic acid encodes a light chain constant domain further comprising a leucine at residue 133 (133L); said second nucleic acid encodes a light chain constant domain further comprising a glutamine or aspartic acid at residue 174 (174Q or 174D), and said third nucleic acid encodes a heavy chain variable domain further comprising an arginine at residue 105 (105R) with said fourth nucleic acid encoding a light chain variable domain further comprising an aspartic acid at residue 42 (42D).
  • a method for producing a fragment, antigen binding comprising: (1) co-expressing in a host cell: (a) a first nucleic acid encoding both a heavy chain variable domain and an IgG heavy chain constant CH1 domain, wherein said heavy chain variable domain comprises a lysine at residue 39 (39K) and a glutamic acid at the residue which is four amino acids upstream of the first residue of HFR3 according to Kabat, and said heavy chain CH1 domain comprises an alanine at residue 172 (172A) and a glycine at residue 174 (174G); and (b) a second nucleic acid encoding both a light chain variable domain and a light chain constant domain wherein said light chain variable domain is a kappa isotype and comprises an arginine at residue 1 (1R) and an aspartic acid at residue 38 (38D), and said light chain constant domain comprises a tyrosine at residue 135 (135Y) and a tryptophan at residue 176
  • said first nucleic acid encodes a heavy chain CH1 constant domain further comprising a methionine or isoleucine at residue 190 (190M or 190I); said second nucleic acid encodes a light chain constant domain further comprising a leucine at residue 133 (133L); and said second nucleic acid encodes a light chain constant domain further comprising a glutamine or aspartic acid at residue 174 (174Q or 174D).
  • a method for producing a fragment, antigen binding comprising: (1) co-expressing in a host cell: (a) a first nucleic acid encoding both a heavy chain variable domain and an IgG heavy chain constant CH1 domain, wherein said heavy chain variable domain comprises a lysine at residue 39 (39K) and a glutamic acid at the residue which is four amino acids upstream of the first residue of HFR3 according to Kabat, and said heavy chain CH1 domain comprises an arginine at residue 172 (172R) and a glycine at residue 174 (174G); and (b) a second nucleic acid encoding both a light chain variable domain and a light chain constant domain wherein said light chain variable domain is a kappa isotype and comprises an arginine at residue 1 (1R) and an aspartic acid at residue 38 (38D), and said light chain constant domain comprises a tyrosine at residue 135 (135Y) and a tryptophan at residue
  • said first nucleic acid encodes a heavy chain CH1 constant domain further comprising a methionine or isoleucine at residue 190 (190M or 190I); said second nucleic acid encodes a light chain constant domain further comprising a leucine at residue 133 (133L); and said second nucleic acid encodes a light chain constant domain further comprising a glutamine or aspartic acid at residue 174 (174Q or 174D).
  • a method for producing a fragment, antigen binding comprising: (1) co-expressing in a host cell: (a) a first nucleic acid encoding both a heavy chain variable domain and an IgG heavy chain constant CH1 domain, wherein said heavy chain variable domain comprises a lysine at residue 39 (39K) and a glutamic acid at the residue which is four amino acids upstream of the first residue of HFR3 according to Kabat, and said heavy chain CH1 domain comprises an alanine at residue 172 (172A) and a glycine at residue 174 (174G); and (b) a second nucleic acid encoding both a light chain variable domain and a light chain constant domain wherein said light chain variable domain is a kappa isotype and comprises an arginine at residue 1 (1R) and an aspartic acid at residue 38 (38D), and said light chain constant domain comprises a phenylalanine at residue 135 (135F) and a tryptophan at
  • a method for producing a fragment, antigen binding comprising: (1) co-expressing in a host cell: (a) a first nucleic acid encoding both a heavy chain variable domain and an IgG heavy chain constant CH1 domain, wherein said heavy chain variable domain comprises a tyrosine at residue 39 (39Y) and said heavy chain CH1 domain comprises a WT sequence; and (b) a second nucleic acid encoding both a light chain variable domain and a light chain constant domain wherein said light chain variable domain comprises an arginine at residue 38 (38R) and said light chain constant domain comprises a WT sequence, wherein each of said heavy chain and light chain variable domains comprise three complementarity determining regions (CDRs) which direct binding to the same antigen; (2) cultivating said host cell under conditions such that said heavy chain variable and constant domains and said light chain variable and constant domains are produced; and (3) recovering from said host cell a Fab comprising said heavy chain variable and constant domains and said light chain variable and
  • said first nucleic acid encodes a heavy chain variable domain further comprising an arginine at residue 105 (105R) and said second nucleic acid encodes a light chain variable domain further comprising an aspartic acid at residue 42 (42D).
  • a method for producing a fragment, antigen binding comprising: (1) co-expressing in a host cell: (a) a first nucleic acid encoding both a heavy chain variable domain and an IgG heavy chain constant CH1 domain, wherein said heavy chain variable domain comprises a tyrosine at residue 39 (39Y) and said heavy chain CH1 domain comprises an aspartic acid at residue 228 (228D); and (b) a second nucleic acid encoding both a light chain variable domain and a light chain constant domain wherein said light chain variable domain comprises an arginine at residue 38 (38R) and said light chain constant domain comprises a lysine at residue 122 (122K), wherein each of said heavy chain and light chain variable domains comprise three complementarity determining regions (CDRs) which direct binding to the same antigen; (2) cultivating said host cell under conditions such that said heavy chain variable and constant domains and said light chain variable and constant domains are produced; and (3) recovering from said host cell a Fab comprising: (1) co-expressing in
  • said first nucleic acid encodes a heavy chain variable domain further comprising an arginine at residue 105 (105R) and said second nucleic acid encodes a light chain variable domain further comprising an aspartic acid at residue 42 (42D).
  • a method for producing a fragment, antigen binding comprising: (1) co-expressing in a host cell: (a) a first nucleic acid encoding both a heavy chain variable domain and an IgG heavy chain constant CH1 domain, wherein said heavy chain variable domain comprises a lysine at residue 39 (39K) and a glutamic acid at the residue which is four amino acids upstream of the first residue of HFR3 according to Kabat, and said heavy chain CH1 domain comprises a WT sequence; and (b) a second nucleic acid encoding both a light chain variable domain and a light chain constant domain wherein said light chain variable domain is a kappa isotype and comprises an arginine at residue 1 (1R) and an aspartic acid at residue 38 (38D), and said light chain constant domain comprises a WT sequence, wherein each of said heavy chain and light chain variable domains comprise three complementarity determining regions (CDRs) which direct binding to the same antigen; (2) cultivating said host
  • a method for producing a fragment, antigen binding comprising: (1) co-expressing in a host cell: (a) a first nucleic acid encoding both a heavy chain variable domain and an IgG heavy chain constant CH1 domain, wherein said heavy chain variable domain comprises a lysine at residue 39 (39K) and a glutamic acid at the residue which is four amino acids upstream of the first residue of HFR3 according to Kabat, and said IgG heavy chain constant CH1 domain comprises an aspartic acid at residue 228 (228D); and (b) a second nucleic acid encoding both a light chain variable domain and a light chain constant domain wherein said light chain variable domain is a kappa isotype and comprises an arginine at residue 1 (1R) and an aspartic acid at residue 38 (38D) and said light chain constant domain comprises a lysine at residue 122 (122K), wherein each of said heavy chain and light chain variable domains comprise three complementarity determining
  • a method for producing a fragment, antigen binding comprising: (1) co-expressing in a host cell: (a) a first nucleic acid encoding both a heavy chain variable domain and an IgG heavy chain constant CH1 domain, wherein said heavy chain variable domain comprises a tyrosine at residue 39 (39Y) and said heavy chain CH1 domain comprises an alanine at residue 172 (172A) and a glycine at residue 174 (174G) ; and (b) a second nucleic acid encoding both a light chain variable domain and a light chain constant domain wherein said light chain variable domain comprises an arginine at residue 38 (38R) and said light chain constant domain comprises a tyrosine at residue 135 (135Y) and a tryptophan at residue 176 (176W), wherein each of said heavy chain and light chain variable domains comprise three complementarity determining regions (CDRs) which direct binding to the same antigen; (2) cultivating said host cell under conditions such
  • said first nucleic acid encodes a heavy chain variable domain further comprising an arginine at residue 105 (105R) and said second nucleic acid encodes a light chain variable domain further comprising an aspartic acid at residue 42 (42D).
  • a method for producing a first and second fragment, antigen binding comprising: (1) co-expressing in a host cell: (a) a first nucleic acid encoding both a first heavy chain variable domain and a first IgG heavy chain constant CH1 domain, wherein said first heavy chain variable domain comprises a lysine at residue 39 (39K) and a glutamic acid at the residue which is four amino acids upstream of the first residue of HFR3 according to Kabat, and said first IgG heavy chain constant CH1 domain comprises an arginine at residue 172 (172R) and a glycine at residue 174 (174G); (b) a second nucleic acid encoding both a first light chain variable domain and a first light chain constant domain, wherein said first light chain variable domain is a kappa isotype and comprises an arginine at residue 1 (1R) and an aspartic acid at residue 38 (38D), and said first light chain constant domain comprises a tyrosine at
  • said first nucleic acid encodes a heavy chain CH1 constant domain further comprising a methionine or isoleucine at residue 190 (190M or 190I); said second nucleic acid encodes a light chain constant domain further comprising a leucine at residue 133 (133L); said second nucleic acid encodes a light chain constant domain further comprising a glutamine or aspartic acid at residue 174 (174Q or 174D), and said third nucleic acid encodes a heavy chain variable domain further comprising an arginine at residue 105 (105R) with said fourth nucleic acid encoding a light chain variable domain further comprising an aspartic acid at residue 42 (42D).
  • a method for producing a first and second fragment, antigen binding comprising: (1) co-expressing in a host cell: (a) a first nucleic acid encoding both a first heavy chain variable domain and a first IgG heavy chain constant CH1 domain, wherein said first heavy chain variable domain comprises a lysine at residue 39 (39K) and a glutamic acid at the residue which is four amino acids upstream of the first residue of HFR3 according to Kabat, and said first IgG heavy chain constant CH1 domain comprises an alanine at residue 172 (172A) and a glycine at residue 174 (174G); (b) a second nucleic acid encoding both a first light chain variable domain and a first light chain constant domain, wherein said first light chain variable domain is a kappa isotype and comprises an arginine at residue 1 (1R) and an aspartic acid at residue 38 (38D), and said first light chain constant domain comprises a tyrosine at
  • said first nucleic acid encodes a heavy chain CH1 constant domain further comprising a methionine or isoleucine at residue 190 (190M or 190I); said second nucleic acid encodes a light chain constant domain further comprising a leucine at residue 133 (133L); said second nucleic acid encodes a light chain constant domain further comprising a glutamine or aspartic acid at residue 174 (174Q or 174D), and said third nucleic acid encodes a heavy chain variable domain further comprising an arginie at residue 105 (105R) with said fourth nucleic acid encoding a light chain variable domain further comprising an aspartic acid at residue 42 (42D).
  • a method for producing a first and second fragment, antigen binding comprising: (1) co-expressing in a host cell: (a) a first nucleic acid encoding both a first heavy chain variable domain and a first IgG heavy chain constant CH1 domain, wherein said first heavy chain variable domain comprises a lysine at residue 39 (39K) and a glutamic acid at the residue which is four amino acids upstream of the first residue of HFR3 according to Kabat, and said first IgG heavy chain constant CH1 domain comprises an arginine at residue 172 (172R) and a glycine at residue 174 (174G); (b) a second nucleic acid encoding both a first light chain variable domain and a first light chain constant domain, wherein said first light chain variable domain is a kappa isotype and comprises an arginine at residue 1 (1R) and an aspartic acid at residue 38 (38D), and said first light chain constant domain comprises a tyrosine at
  • said first nucleic acid encodes a heavy chain CH1 constant domain further comprising a methionine or isoleucine at residue 190 (190M or 190I); said second nucleic acid encodes a light chain constant domain further comprising a leucine at residue 133 (133L); said second nucleic acid encodes a light chain constant domain further comprising a glutamine or aspartic acid at residue 174 (174Q or 174D), and said third nucleic acid encodes a heavy chain variable domain further comprising an arginine at residue 105 (105R) with said fourth nucleic acid encoding a light chain variable domain further comprising an aspartic acid at residue 42 (42D).
  • a method for producing a first and second fragment, antigen binding comprising: (1) co-expressing in a host cell: (a) a first nucleic acid encoding both a first heavy chain variable domain and a first IgG heavy chain constant CH1 domain, wherein said first heavy chain variable domain comprises a lysine at residue 39 (39K) and a glutamic acid at the residue which is four amino acids upstream of the first residue of HFR3 according to Kabat, and said first IgG heavy chain constant CH1 domain comprises an alanine at residue 172 (172A) and a glycine at residue 174 (174G); (b) a second nucleic acid encoding both a first light chain variable domain and a first light chain constant domain, wherein said first light chain variable domain is a kappa isotype and comprises an arginine at residue 1(1R) and an aspartic acid at residue 38 (38D), and said first light chain constant domain comprises a phenylalan
  • a method for producing a first and second fragment, antigen binding comprising: (1) co-expressing in a host cell: (a) a first nucleic acid encoding both a first heavy chain variable domain and a first IgG heavy chain constant CH1 domain, wherein said first heavy chain variable domain comprises a tyrosine at residue 39 (39Y), and said first IgG heavy chain constant CH1 domain comprises an alanine at residue 172 (172A) and a glycine at residue 174 (174G); (b) a second nucleic acid encoding both a first light chain variable domain and a first light chain constant domain, wherein said first light chain variable domain comprises an arginine at residue 38 (38R), and said first light chain constant domain comprises a tyrosine at residue 135 (135Y) and a tryptophan at residue 176 (176W); (c) a third nucleic acid encoding both a second heavy chain variable domain and a second IgG heavy chain
  • said first nucleic acid encodes a heavy chain variable domain further comprising an arginine at residue 105 (105R) and said second nucleic acid encodes a light chain variable domain further comprising an aspartic acid at residue 42 (42D).
  • a method for producing a first and second fragment, antigen binding comprising: (1) co-expressing in a host cell: (a) a first nucleic acid encoding both a first heavy chain variable domain and a first IgG heavy chain constant CH1 domain, wherein said first heavy chain variable domain comprises a tyrosine at residue 39 (39Y), and said first IgG heavy chain constant CH1 domain comprises an alanine at residue 172 (172A) and a glycine at residue 174 (174G); (b) a second nucleic acid encoding both a first light chain variable domain and a first light chain constant domain, wherein said first light chain variable domain comprises an arginine at residue 38 (38R), and said first light chain constant domain comprises a tyrosine at residue 135 (135Y) and a tryptophan at residue 176 (176W); (c) a third nucleic acid encoding both a second heavy chain variable domain and a second IgG heavy chain
  • said first nucleic acid encodes a heavy chain variable domain further comprising an arginine at residue 105 (105R) and said second nucleic acid encodes a light chain variable domain further comprising an aspartic acid at residue 42 (42D).
  • a method for producing a bispecific antibody comprising: (1) co-expressing in a host cell: (a) a first nucleic acid encoding a first IgG heavy chain, wherein said first heavy chain comprises a variable domain comprising a lysine at residue 39 (39K) and a glutamic acid at the residue which is 4 amino acids upstream of the first residue of HFR3 according to Kabat, and a CH1 constant domain comprising an arginine at residue 172 (172R) and a glycine at residue 174 (174G); (b) a second nucleic acid encoding a first light chain, wherein said first light chain comprises a kappa variable domain comprising an arginine at residue 1 (1R) and an aspartic acid at residue 38 (38D), and a constant domain comprising a tyrosine at residue 135 (135Y) and a tryptophan at residue 176 (176W); (c) a third nucleic acid encoding
  • said first nucleic acid encodes a heavy chain CH1 constant domain further comprising a methionine or isoleucine at residue 190 (190M or 190I); said second nucleic acid encodes a light chain constant domain further comprising a leucine at residue 133 (133L); said second nucleic acid encodes a light chain constant domain further comprising a glutamine or aspartic acid at residue 174 (174Q or 174D), and said third nucleic acid encodes a heavy chain variable domain further comprising an arginine at residue 105 (105R) with said fourth nucleic acid encoding a light chain variable domain further comprising an aspartic acid at residue 42 (42D).
  • a method for producing a bispecific antibody comprising: (1) co-expressing in a host cell: (a) a first nucleic acid encoding a first IgG heavy chain, wherein said first heavy chain comprises a variable domain comprising a lysine at residue 39 (39K) and a glutamic acid at the residue which is four amino acids upstream of the first residue of HFR3 according to Kabat, and a CH1 constant domain comprising an alanine at residue 172 (172A) and a glycine at residue 174 (174G); (b) a second nucleic acid encoding a first light chain, wherein said first light chain comprises a kappa variable domain comprising an arginine at residue 1 (1R) and an aspartic acid at residue 38 (38D), and a constant domain comprising a tyrosine at residue 135 (135Y) and a tryptophan at residue 176 (176W); (c) a third nucleic acid encoding
  • said first nucleic acid encodes a heavy chain CH1 constant domain further comprising a methionine or isoleucine at residue 190 (190M or 190I); said second nucleic acid encodes a light chain constant domain further comprising a leucine at residue 133 (133L); said second nucleic acid encodes a light chain constant domain further comprising a glutamine or aspartic acid at residue 174 (174Q or 174D), and said third nucleic acid encodes a heavy chain variable domain further comprising an arginine at residue 105 (105R) with said fourth nucleic acid encoding a light chain variable domain further comprising an aspartic acid at residue 42 (42D).
  • a method for producing a bispecific antibody comprising: (1) co-expressing in a host cell: (a) a first nucleic acid encoding a first IgG heavy chain, wherein said first heavy chain comprises a variable domain comprising a lysine at residue 39 (39K) and a glutamic acid at the residue which is four amino acids upstream of the first residue of HFR3 according to Kabat, and a CH1 constant domain comprising an arginine at residue 172 (172R) and a glycine at residue 174 (174G); (b) a second nucleic acid encoding a first light chain, wherein said first light chain comprises a kappa variable domain comprising an arginine at residue 1 (1R) and an aspartic acid at residue 38 (38D), and a constant domain comprising a tyrosine at residue 135 (135Y) and a tryptophan at residue 176 (176W); (c) a third nucleic acid encoding
  • said first nucleic acid encodes a heavy chain CH1 constant domain further comprising a methionine or isoleucine at residue 190 (190M or 190I); said second nucleic acid encodes a light chain constant domain further comprising a leucine at residue 133 (133L); said second nucleic acid encodes a light chain constant domain further comprising a glutamine or aspartic acid at residue 174 (174Q or 174D), and said third nucleic acid encodes a heavy chain variable domain further comprising an arginine at residue 105 (105R) with said fourth nucleic acid encoding a light chain variable domain further comprising an aspartic acid at residue 42 (42D).
  • a method for producing a bispecific antibody comprising: (1) co-expressing in a host cell: (a) a first nucleic acid encoding a first IgG heavy chain, wherein said first heavy chain comprises a variable domain comprising a tyrosine at residue 39 (39Y), and a CH1 constant domain comprising an alanine at residue 172 (172A) and a glycine at residue 174 (174G); (b) a second nucleic acid encoding a first light chain, wherein said first light chain comprises a variable domain comprising an arginine at residue 38 (38R), and a constant domain comprising a tyrosine at residue 135 (135Y) and a tryptophan at residue 176 (176W); (c) a third nucleic acid encoding a second IgG heavy chain, wherein said heavy chain comprises a variable domain comprising a lysine at residue 39 (39K) and a glutamic acid at the residue which is
  • said first nucleic acid encodes a heavy chain variable domain further comprising an arginine at residue 105 (105R) and said second nucleic acid encodes a light chain variable domain further comprising an aspartic acid at residue 42 (42D).
  • a method for producing a bispecific antibody comprising: (1) co-expressing in a host cell: (a) a first nucleic acid encoding a first IgG heavy chain, wherein said first heavy chain comprises a variable domain comprising a tyrosine at residue 39 (39Y), and a CH1 constant domain comprising an alanine at residue 172 (172A) and a glycine at residue 174 (174G); (b) a second nucleic acid encoding a first light chain, wherein said first light chain comprises a variable domain comprising an arginine at residue 38 (38R), and a constant domain comprising a tyrosine at residue 135 (135Y) and a tryptophan at residue 176 (176W); (c) a third nucleic acid encoding a second IgG heavy chain, wherein said heavy chain comprises a variable domain comprising a lysine at residue 39 (39K) and a glutamic acid at the residue which is
  • said first nucleic acid encodes a heavy chain variable domain further comprising an arginine at residue 105 (105R) and said second nucleic acid encodes a light chain variable domain further comprising an aspartic acid at residue 42 (42D).
  • the present invention provides a method wherein one of said first and second IgG heavy chains further comprises a CH3 constant domain comprising a lysine at residue 356 and a lysine at residue 399, and the other of said first and second IgG heavy chains further comprises a CH3 constant domain comprising an aspartic acid at residue 392 and an aspartic acid at residue 409.
  • a method for producing a bispecific antibody comprising: (1) co-expressing in a host cell: (a) a first nucleic acid encoding a first IgG heavy chain, wherein said first heavy chain comprises a variable domain comprising a lysine at residue 39 (39K) and a glutamic acid at the residue which is four amino acids upstream of the first residue of HFR3 according to Kabat, a CH1 constant domain comprising an alanine at residue 172 (172A) and a glycine at residue 174 (174G) and a CH3 constant domain comprising a lysine at residue 356 (356K) and a lysine at residue 399 (399K); (b) a second nucleic acid encoding a first light chain, wherein said first light chain comprises a kappa variable domain comprising an arginine at residue 1 (1R) and an aspartic acid at residue 38 (38D), and a constant domain comprising a ty
  • the host cell for use in the methods of the present invention is a mammalian cell, more particularly a HEK293 or CHO cell, and the IgG heavy chain constant domain produced by the methods of the present invention is IgG1 or IgG4 isotype, and more particularly IgG1.
  • the present invention provides Fabs and bi-specific antibodies, each produced according to the methods of the present invention.
  • host cells comprising nucleic acids encoding the same.
  • the present invention provides any of the Fabs and bispecific antibodies as exemplified in any of the Examples herein.
  • a bispecific antibody comprising a first IgG heavy chain, wherein said first heavy chain comprises a variable domain comprising a lysine at residue 39 (39K) and a glutamic acid at the residue which is four amino acids upstream of the first residue of HFR3 according to Kabat, a CH1 constant domain comprising an alanine at residue 172 (172A) and a glycine at residue 174 (174G) and a CH3 constant domain comprising a lysine at residue 356 (356K) and a lysine at residue 399 (399K); (b) a first light chain, wherein said first light chain comprises a kappa variable domain comprising an arginine at residue 1 (1R) and an aspartic acid at residue 38 (38D), and a constant domain comprising a tyrosine at residue 135 (135Y) and a tryptophan at residue 176 (176W); (c) a second IgG heavy chain, wherein said first light chain comprises a
  • an "antibody” For a full length antibody of the IgG type, there are four amino acid chains (two “heavy” chains and two “light” chains) that are cross-linked via intra- and inter-chain disulfide bonds. When expressed in certain biological systems, e.g. mammalian cell lines, antibodies having unmodified human Fc sequences are glycosylated in the Fc region. Antibodies may be glycosylated at other positions as well.
  • the subunit structures and three-dimensional configurations of antibodies are well known. Each heavy chain is comprised of an N-terminal heavy chain variable region ("V H ”) and a heavy chain constant region ("C H ").
  • the heavy chain constant region is comprised of three domains (C H 1, C H 2, and C H 3) for IgG as well as a hinge region ("hinge") between the C H1 and C H2 domains.
  • Each light chain is comprised of a light chain variable region ("V L ”) and a light chain constant region ("C L ").
  • the C L and V L regions may be of the kappa (" ⁇ ") or lambda (" ⁇ ") isotypes.
  • IgG antibodies can be further divided into subclasses, e.g., IgG1, IgG2, IgG3, IgG4, as appreciated by one of skill in the art
  • variable regions of each heavy chain - light chain pair associate to form binding sites.
  • the heavy chain variable region (V H ) and the light chain variable region (V L ) can be subdivided into regions of hypervariability, termed complementarity determining regions ("CDRs"), interspersed with regions that are more conserved, termed framework regions ("FR").
  • CDRs complementarity determining regions
  • FR framework regions
  • Each V H and V L is composed of three CDRs and four FRs, arranged from amino-terminus to carboxy-terminus in the following order: FR1, CDR1, FR2, CDR2, FR3, CDR3, FR4.
  • CDRH1, CDRH2, and CDRH3 CDRH1, CDRH2, and CDRH3
  • CDRL1, CDRL2 and CDRL3 3 CDRs of the light chain
  • the FRs of the heavy chain may be referred to as HFR1, HFR2, HFR3 and HFR4
  • the FRs of the light chain may be referred to as LFR1, LFR2, LFR3 and LFR4.
  • the CDRs contain most of the residues which form specific interactions with the antigen
  • a wild type IgG antibody contains two identical fragments termed "fragment, antigen binding” (or Fab), each of which is composed of the V H and C H 1 domains of one heavy chain and the V L and C L domains of a light chain. Each Fab directs binding of the antibody to the same antigen.
  • fragment, antigen binding or Fab
  • IgG BsAb refers to an IgG antibody comprising two distinct Fabs, each of which direct binding to a separate antigen, and composed of two distinct heavy chains and two distinct light chains.
  • V H and C H 1 domains of one heavy chain associate with the V L and C L domains of one light chain to form a "first" Fab
  • V H and C H 1 domains of the other heavy chain associate with the V L and C L domains of the other light chain to form a "second" Fab.
  • bi-specific antibody refers to an IgG1, IgG2 or IgG4 class of bi-specific antibody.
  • the term "bi-specific antibody” refers to an IgG1 or IgG4 class of bi-specific antibody, and most particularly an IgG1 class.
  • bi-specific antigen binding compound refers to Fab-Fab and IgG-Fab molecules.
  • Figure 1 included herein, provides a schematic diagram of the structure of bi-specific antibodies (IgG BsAb) as well as the Fab-Fab and IgG-Fab formats contemplated by the methods and compounds of the present invention.
  • the methods and compounds of the present invention comprise designed amino acid modifications at particular residues within the variable and constant domains of heavy chain and light chain polypeptides.
  • various numbering conventions may be employed for designating particular amino acid residues within IgG variable region sequences. Commonly used numbering conventions include Kabat and EU index numbering (see, Kabat et al., Sequences of Proteins of Immunological Interest, 5th Ed, Public Health Service, National Institutes of Health, Bethesda, MD (1991 )).
  • Other conventions that include corrections or alternate numbering systems for variable domains include Chothia ( Chothia C, Lesk AM (1987), JMol Biol 196: 901-917 ; Chothia, et al.
  • CDR sequence length may vary between individual IgG molecules and, further, the numbering of individual residues within a CDR may vary depending on the numbering convention applied.
  • the disclosure of the present invention first employs Kabat to identify the N-terminal (first) amino acid of the HFR3.
  • the amino acid residue to be modified is then designated as being four (4) amino acid residues upstream (i.e. in the N-terminal direction) from the first amino acid in the reference HFR3.
  • Design A of the present invention comprises the replacement of a WT amino acid in HCDR2 with a glutamic acid (E).
  • amino acid residue X66 is the most N-terminal (first) amino acid residue of variable region heavy chain framework three (HFR3).
  • HFR3 variable region heavy chain framework three
  • One of ordinary skill can employ such a strategy to identify the first amino acid residue (most N-terminal) of heavy chain framework three (HFR3) from any human IgG1 or IgG4 variable region. Once this landmark is determined, one can then locate the amino acid four residues upstream (N-terminal) to this location and replace that amino acid residue (using standard insertion/deletion methods) with a glutamic acid (E) to achieve the "Design A" modification of the invention.
  • a/an [amino acid name] substituted at residue .. .” refers to substitution of the parental amino acid with the indicated amino acid.
  • a heavy chain comprising "a lysine substituted at residue 39” refers to a heavy chain wherein the parental amino acid sequence has been mutated to contain a lysine at residue number 39 in place of the parental amino acid.
  • Such mutations may also be represented by denoting a particular amino acid residue number, preceded by the parental amino acid and followed by the replacement amino acid.
  • “Q39K” refers to a replacement of a glutamine at residue 39 with a lysine.
  • 39K refers to replacement of a parental amino acid with a lysine.
  • an antibody or Fab of the present invention may be derived from a single copy or clone (e.g. a monoclonal antibody (mAb)), including any eukaryotic, prokaryotic, or phage clone.
  • a compound of the present invention exists in a homogeneous or substantially homogeneous population.
  • the antibody, Fab or other antigen binding compound, or a nucleic acid encoding the same is provided in "isolated” form.
  • isolated refers to a protein, peptide or nucleic acid which is free or substantially free from other macromolecular species found in a cellular environment.
  • a compound as disclosed herein can be produced using techniques well known in the art, e.g., recombinant technologies, phage display technologies, synthetic technologies or combinations of such technologies or other technologies readily known in the art. In particular, the methods and procedures of the Examples herein may be readily employed.
  • An antibody or Fab of the present invention may be further engineered to comprise framework regions derived from fully human frameworks. A variety of different human framework sequences may be used in carrying out embodiments of the present invention.
  • the framework regions of a compound of the present invention are of human origin or are substantially human (at least 95%, 97% or 99% of human origin.)
  • the sequences of framework regions of human origin may be obtained from The Immunoglobulin Factsbook, by Marie-Paule Lefranc, Gerard Lefranc, Academic Press 2001, ISBN 012441351 .
  • Expression vectors capable of directing expression of genes to which they are operably linked are well known in the art.
  • Expression vectors can encode a signal peptide that facilitates secretion of the desired polypeptide product(s) from a host cell.
  • the signal peptide can be an immunoglobulin signal peptide or a heterologous signal peptide.
  • Desired polypeptides for example the components of the bi-specific antibodies or Fabs prepared according to the methods of the present invention, may be expressed independently using different promoters to which they are operably linked in a single vector or, alternatively, the desired products may be expressed independently using different promoters to which they are operably linked in separate vectors.
  • a "host cell” refers to a cell that is stably or transiently transfected, transformed, transduced or infected with nucleotide sequences encoding a desired polypeptide product or products. Creation and isolation of host cell lines producing a bi-specific antibody, Fab or other antigen binding compound of the present invention can be accomplished using standard techniques known in the art.
  • Mammalian cells are preferred host cells for expression of the Fabs or bi-specific antibodies according to the present invention.
  • Particular mammalian cells are HEK 293, NS0, DG-44, and CHO cells.
  • expressed polypeptides are secreted into the medium in which the host cells are cultured, from which the polypeptides can be recovered isolated.
  • Medium, into which an expressed polypeptide has been secreted may be purified by conventional techniques.
  • the medium may be applied to and eluted from a Protein A or G column using conventional methods. Soluble aggregate and multimers may be effectively removed by common techniques, including size exclusion, hydrophobic interaction, ion exchange, or hydroxyapatite chromatography. Recovered products may be immediately frozen, for example at -70°C, or may be lyophilized.
  • Example 1 Computational design to identify modifications of C H 1/C L interface residues that discriminate between designed and native immunoglobulin C H 1/C L interfaces.
  • Residues for initial modification at the C H 1/C L interface are selected using a combination of computational and rational design strategies.
  • a crystal structure of the IgG1/ ⁇ Fab (PDB ID 3TV3 ( see , Lewis, S.M. and Kuhlman, B.A. (2011), PLoS ONE 6(6): e20872 )
  • the Rosetta software suite and related modeling applications are employed to evolve potential sequences for modification according to a desired fitness function ( see , Kaufmann et al. (2010), Biochemistry 49; 2987-2998 ; Leaver-Fay et al.(2011), Methods Enzymol.
  • Rosetta calculates a fitness score and binding energy based on a weighted sum of energy potentials treating phenomena such as van der Waals forces and hydrogen bonding forces. Overall, the summations of these different parameters are measured in units known as the Rosetta Energy Unit (REU). These values are interpreted as free energies, but are not directly translatable into typical units of energy.
  • REU Rosetta Energy Unit
  • the identified mutations are subjected to computational re-docking of the C H 1/C L complex using RosettaDock via RosettaScripts ( see , Chaudhury et al.(2011), PLoS ONE 6(8): e2247 and Fleishman et al.(2011), PLoS ONE 6(6): e20161 ). This allows determination of optimal binding positions for designed complexes and allows comparison with binding energies of the similarly docked WT complexes and the undesired designed-C H 1/WT-C L and WT-C H 1/designed-C L complexes.
  • H_F174T indicates that residue 174 of the heavy chain is modified from a phenylalanine (F) to a threonine (T).
  • a pertuzumab see , Nahta et al.(2004), Cancer Res. 64; 2343-2346 ) human IgG1 with a human chimeric kappa V L and lambda C L (C ⁇ .) is created.
  • the pertuzumab V H domain insert is generated using a PCR-based overlapping oligonucleotide synthesis procedure ( Casimiro et al. (1997), Structure 5; 1407-1412 ) using the sequence from the published crystal structure ( Franklin et al.(2004), Cancer Cell 5; 317-328 ).
  • the insert contains appropriate AgeI and NheI restriction sites that enable it to be ligated directly into a linearized in-house pE vector (Lonza) containing an IgG1 constant domain sequence.
  • the pertuzumab V L gene is also generated using overlapping oligonucleotide synthesis.
  • a DNA sequence encoding the V L domain fused to C ⁇ is constructed using PCR and an in-house plasmid template containing the C ⁇ sequence. Both 5' and 3' flanking oligonucleotides and two internal primers are designed to anneal the C-terminus of the pertuzumab V L domain to the N-terminus of C ⁇ .
  • the light chain insert is designed with HindIII and EcoRI restriction sites for direct ligation into a linearized in-house pE vector (Lonza) with a selectable GS marker system.
  • Each pE mammalian expression vector is engineered to contain a common mouse antibody light chain signal sequence that is translated in-frame as part of the expressed protein and cleaved prior to secretion. All ligation constructs are transformed into E. coli strain TOP 10 competent cells (Life Technologies). Transformed bacterial colonies are picked, cultured, and the plasmids are prepped. Correct sequences are confirmed by DNA sequencing.
  • the encoded sequences of the mature heavy chain and light chain proteins are given by SEQ ID NO:1 and SEQ ID NO:2, respectively.
  • variable domains which, if present, add complexity to the data interpretation. Therefore, human IgG1 and human lambda constructs lacking variable genes (V H and V L ) are constructed. A recombinase-based subcloning strategy is used to remove the variable genes.
  • two double stranded oligonucleotides that encompass 15 base pairs 5' of an XhoI site through the common mouse antibody light chain signal sequence followed immediately by a NheI site and 15 flanking base pairs (encoding the N-terminus of the IgG1 C H 1 domain for efficient recombination) are chemically synthesized.
  • This double stranded oligonucleotide pair has the V H domain deleted.
  • variable genes are digested out of the parental pertuzumab heavy chain and ight chain plasmids using the XhoI/NheI and BamHI/XmaI enzymes, respectively.
  • the corresponding oligonucleotide pairs are inserted into the linearized plasmids using the recombinase-based In-Fusion HD Cloning kit (Clontech) according to the manufacturer's protocol.
  • the sequences of the heavy chain and light chain IgG1/ ⁇ constructs lacking variable domains are given by SEQ ID NO: 3 and SEQ ID NO: 4, respectively.
  • the QuikChange II Site Directed Mutagenesis Kit (Agilent) may be used following the instructions provided by the manufacturer.
  • a gene synthesis strategy may be employed (G-blocks, IDT).
  • the synthesized genes are designed to be compatible with the heavy chain and light chain construct lacking variable domains (described above). However, within the heavy chain construct, an Xho I site upstream of the common mouse light chain signal sequence is deleted using site directed mutagenesis and a new Xho I site is generated at the C-terminus (3' end) of the coding region of the C H 1 domain.
  • Synthesized genes are ligated to the heavy chain plasmid using the NheI and new XhoI restriction sites. Synthesized genes are added to the light chain plasmid using the BamHI and EcoRI restriction sites.
  • Each plasmid is scaled-up by transformation into TOP10 E. coli , mixed with 100 mL luria broth in a 250 mL baffled flask, and shaken O/N at 220 rpm. Large scale plasmid purifications are performed using the BenchPro 2100 (Life Technologies) according to the manufacturer's instructions.
  • plasmids harboring the heavy chain and light chain DNA sequences are transfected (1:2 plasmid ratio for the heavy chain and light chain plasmids, respectively) into HEK293F cells using Freestyle transfection reagents and protocols provided by the manufacturer (Life Technologies). Transfected cells are grown at 37 °C in a 5% CO 2 incubator while shaking at 125 rpm for 5 days. Secreted protein is harvested by centrifugation at 10 K rpm for 5 min. Supernatants are passed through 2 ⁇ m filters (both large scale and small scale) for purification.
  • the concentration of the purified proteins are determined by measuring the absorbance of the solutions at 280 nm using a NanoDrop UV-Vis spectrophotometer from Thermo Scientific ( Grimsley, G.R. and Pace, C.N.(2004), Curr. Protoc. Protein Sci., Ch. 3 (3.1 )).
  • the proteins may be characterized using multiple methods, as described herein. For example, sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) analyses are used to evaluate expression and assembly of the HC and LC components. SDS-PAGE may be performed using NuPAGE® Novex 4-12% BisTris gels according to manufacturer protocols (Life Technologies). Approximately 15 ⁇ L of purified material from the magnetic bead purifications (see above) are loaded in each well. For reduced samples, 10% 0.5 M DTT in H 2 O is added. Protein bands on the gels are detected using a SimplyBlueTM Safe Stain (Life Technologies).
  • SDS-PAGE sodium dodecyl sulfate polyacrylamide gel electrophoresis
  • Enzyme-linked immunosorbent assays for the detection of thermo-challenged protein samples may also be performed to compare the stability of the designed samples against the wild-type control proteins and the mis-matched designs.
  • T 50 values defined as the temperature at which 50% of the ELISA signal that detects protein activity remains, after heating at elevated temperature for a specified period of time, can be determined for each sample to compare the stability of the designed HC/LC constructs relative to the stability of wild-type controls and mis-matched pairs.
  • 96-well U-bottom high protein binding 96-well plates (Greiner bio-one, cat#650061) are coated overnight at 4 °C with 100 ⁇ L/well of a polyclonal anti-human C ⁇ antibody (Southern Biotech, cat#2070-01) at 2 ug/mL in a 0.05 M NaHCO 3 buffer, pH 8.3. The plates are then washed four times with PBS with 0.02% Tween80 (PBST) and blocked for 1 hr with casein (Thermo, cat#37528) at 37 °C.
  • PBST PBS with 0.02% Tween80
  • the plates are washed again followed by the addition of isolated HEK293F culture supernatants containing the pertuzumab IgG1/ ⁇ protein designs (100 ⁇ L/well). Aliquots of each supernatant are pre-exposed to various temperatures for 1 hr using a PCR instrument with a 25 °C thermal gradient window. The thermal challenged pertuzumab IgG1/ ⁇ proteins (with or without mutations in the C H 1/C L domains) are incubated on the plate for 1 hr at 37 °C.
  • the plates are then washed and 200 ng/mL in-house biotinylated human HER-2-Fc (R&D systems, cat#1 129-ER-020) is added at 100 ⁇ L/well (diluted in casein) for 1 hr at 37 °C.
  • the plates are washed again followed by the addition of streptavidin-HRP (Jackson Immunoresearch, cat#016-030-084) diluted 1:2000 in casein.
  • the plates are then washed and SureBlue Reserve TMB 1-component substrate (KPL, cat#53-00-01) is added at 100 ⁇ L/well. The reaction is allowed to proceed for 5-15 minutes then quenched by the addition of 1% H 3 PO 4 .
  • thermochallenged IgG1/ ⁇ minus variable gene proteins using a polyclonal anti-human C H 1 antibody (2 ⁇ g/mL in casein; Meridian Life Sciences, cat#W90075C) to capture proteins from the supernatants and a HRP-labeled polyclonal anti-human C ⁇ . antibody (1:2000 dilution in casein; Southern Biotech, cat#2070-05) for detection (replacing the HER-2-Fc-biotin and streptavidin-HRP).
  • WT control Titer a ((HCmut/ LCwt b ) vs WT Control) Titer a ((HCwt/ LCmut b ) vs WT Control) SDS-PAGE Assembly c T 5 (°C) T 50 (°C) HCmut/ LCwt T 50 (°C) HCwt/ LCmut WT Pertuzumab IgG1/ ⁇ None 1.0 n.d. d n.d. + 66 n.d. n.d. WT IgG1/C ⁇ minus V-genes None 1.0 n.d. n.d. + 78 n.d. n.d.
  • Titer values are given as a ratio of expression of the indicated designed construct or mis-matched pair (i.e. HC mut/LC wt or HC wt/LC mut) relative to expression of the appropriate WT contol.
  • the mis-matched pairs were expressed separately by co-transfection of a designed HC or LC with a wild-type LC or HC, repectively.
  • c Assembly denoted by single band at 100 kDa by SDS-PAGE (+). Partial assembly denoted by multiple bands on SDS-PAGE including 100 kDa band (+/-). No band at 100 kDa on SDS-PAGE denoted by (-).
  • d n.d. not determined.
  • e Determined in the pertuzumab IgG1 format.
  • f Determined in the IgG1/ ⁇ minus variable genes format.
  • Design 1.0+5.0 maintains a high affinity and stable C H 1/C L interface with low capability for recognizing native immunoglobulin C H 1/C L domains.
  • Design 2.1 demonstrates high stability and specificity for itself while discriminating against binding to native (wt) immunoglobulin C H 1/C L domains.
  • SEC/LS Analytical size exclusion chromatography with in-line light static scattering
  • SEC./LS may be performed for each sample using 30-80 ⁇ L of purified eluant from the small scale-purification described above (concentrations ⁇ 0.1-0.4 mg/mL).
  • the proteins are injected onto a Sepax Zenix SEC 200 analytical HPLC (7.8 ⁇ 300 mm) column equilibrated in 10 mM phosphate, 150 mM NaCl, 0.02% NaN 3 , pH 6.8, using an Agilent 1100 HPLC system.
  • Static light scattering data for material eluted from the SEC column are collected using a miniDAWN TREOS static light scattering detector coupled to an Optilab T-rEX in-line refractive index meter (Wyatt Technologies). UV data are analyzed using HPCHEM (Agilent). Protein molecular weights are determined by their static light scattering profiles using ASTRA V (Wyatt Technologies). SEC/LS analysis indicates that all of the proteins described in Table 3 were shown to be highly monodisperse with soluble aggregates ⁇ 5% and indistinguishable from the wild-type IgG and IgG minus variable domain constructs.
  • Design 2.1 as described in Example 1 , is further optimized to improve specificity of assembly of the designed C H 1/C L interface versus a WT C H 1/C L interface.
  • in-house crystal structures of Design 1.0+5.0 and Design 2.1 are first solved.
  • isolated C H 1/C ⁇ proteins are produced in E. Coli.
  • the isolated C H 1/C ⁇ proteins are subcloned into the pET-DUET plasmid from Novagen.
  • the C H 1 insert (with a pelB signal sequence for secretion into the oxidative periplasmic environment) is synthesized (with a hexahistidine C-terminal tag) using overlapping PCR and subcloned into cassette 1 of the plasmid using the NheI and BamHI sites.
  • the C ⁇ is synthesized (with a hexahistidine C-terminal tag) using overlapping PCR and subcloned into cassette 1 of the plasmid using the NheI and BamHI sites.
  • the culture temperature is reduced to 30 °C and 1 mM Isopropyl-1-thio- ⁇ -D-galactopyranoside is added.
  • the cultures are allowed to grow for 3-4 hrs and harvested by centrifugation for 20 min at 4000 g.
  • the proteins are resuspended in 50 mL of a periplasmic extraction buffer (500 mM sucrose, 100 mM Tris, pH 8, 1 mM EDTA, and 100 ug/mL hen-egg white lysozyme).
  • the extracted proteins are diluted 10-fold into a 10 mM citrate, 10 mM NaCl buffer, pH 5.5 and passed over a 5 mL SP Sepharose FF HiTrap cation exchange column (GE Healthcare) at 5 mL/min using an AKTA Explorer (GE Healthecare).
  • the proteins are eluted from the column using a gradient up to 0.7 M NaCl.
  • the proteins are dialyzed into PBS and captured onto a Ni-Sepharose HiTRAP affinity column.
  • the proteins are then eluted using a gradient up to 0.3 M imidazole.
  • the proteins are then concentrated to ⁇ 3-10 mg/mL using VivaSpin6 centrifugal devices, dialyzed into 10 mM Tris, 100 mM NaCl, pH 8.0 and filtered.
  • the purified proteins are screened using the vapor diffusion crystallization method, whereby protein is first mixed with well solution and deposited in a small chamber with well solution, sealed and allowed to equilibrate with well solution, concentrating both protein and precipitating reagents in the protein drop.
  • Such screens are conducted in a 96-well format (Intelli-plates, Art Robins Instrument) using the commercially available screens: PEGs, PEGs II, ComPAS, Classics, Classics II Suites (Qiagen).
  • the initial setup utilizes a Phoenix robot (Art Robins Instrument), which deposits 0.3 ⁇ L of protein on 0.3 ⁇ L of well solution.
  • Streak seeding using the needle-shaped crystals from the previous step is performed on the following day.
  • Streak seeding is a method promoting crystal nucleation by providing a ready-made nucleus (seed crystals) to assist nucleation and facilitate the growth of ordered crystals.
  • This technique results in a new crystallization condition: 30% PEG4K. Optimizing of this condition is performed at 21 °C by varying the PEG4K concentration, the size of the drop containing the protein and reservoir solution mixture, and the ratio of the protein and reservoir content in the drop. Crystallization drops are seeded and crystals appeared on the next day, growing to the final size within 3 days. Crystals are transferred to a cryo-protection solution of the reservoir solution with PEG4K increased by 10% and supplemented by 20% PEG400 and flash frozen by immersion in liquid nitrogen before shipping to the Advanced Photon Source for data collection.
  • Design 1.0+5.0 is similarly screened and streak-seeded using the WT crystal seeds. Intergrown needle-shaped crystals appeared after 3 days at two conditions: 20% Isopropanol/20% PEG4K/100 mM tri-Sodium Citrate and 33% PEG6K/10 mM tri-Sodium Citrate. Both conditions are optimized, using the technique described above, resulting in single crystals for the optimization of the 2 nd condition.
  • Final Design 1.0+5.0 single crystals are grown at 21 °C by mixing 1.2 ⁇ L of 3.9 mg/ml protein and 1.2 ⁇ L of reservoir solution, containing 40% PEG6K and 10mM tri-Sodium Citrate dehydrate. Crystals are cryo-protected using reservoir solution increased by 10% PEG6K content and supplemented by 20% of Ethylene Glycol.
  • Design 2.1 crystallizes directly in conditions developed for Design 1.0+5.0. Single crystals are grown at 21 °C by mixing 1.5 ⁇ L of 5.1mg/ml protein with 1.5 ⁇ L of reservoir, containing 39% PEG6K and 10mM tri-Sodium Citrate. Crystals are cryoprotected using the same technique as for Design 1.0+5.0.
  • the optimized Design 2.1 proteins are expressed using the transient HEK293F system as described in Example 1. Each of the designs are tested for thermal stability by thermal challenge at temperatures ranging from 70-95 °C using the methodology as described in Example 1. The sustained presence of each design protein after heating is determined using the IgG1/ ⁇ minus variable gene ELISA also as described in Example 1. Results of the thermal challenge stability test for representative optimized designs of Design 2.1 as well as WT IgG1/ C ⁇ . (no V H /V L ) and Design 2.1 are provided below in Table 5.
  • thermochallenge data in Table 5 indicates Design 2.1.3.2, Design 2.1.3.3 and Design 2.1.3.3a were the most stable constructs.
  • a mass spectrometry (MS) method to directly measure the specificity versus the WT C H 1/C L domains is performed. Briefly, at the 2 mL transfection scale, a designed C L domain is co-transfected with a WT C L domain and either a designed heavy chain or a WT heavy chain. In this way the designed and WT C L proteins directly compete with one another during protein expression for binding to the heavy chain protein and secretion into the cell media.
  • the assembled IgG/C L minus variable genes proteins are purified automatically using an Agilent 1100 series HPLC with autosampler and sample collector.
  • the proteins are captured on a PG (protein G) HPLC column (Applied Biosystems, Cat#2-1002-00) at 2 mL/min, washed with phosphate buffered saline (PBS) and eluted with distilled deionized H 2 O, 0.2% formic acid.
  • PBS phosphate buffered saline
  • the protein eluants are concentrated/dried on a Labconco CentriVap Speedvac for 3 hrs at 40 °C under vacuum.
  • the proteins are resuspended in 100 ⁇ L distilled deionized water and neutralized with 20 mL 0.1 M Tris pH 8.0 (MediaTech, Inc., Cat#46-031-CM).
  • the intermolecular disulfides (HC/LC and HC/HC) are reduced by the addition of 10 ⁇ L freshly solubilized 1 M dithiothreitol (DTT, Sigma, Cat#43815-1G).
  • DTT dithiothreitol
  • the samples are sequentially collected using an Agilent 1100 series HPLC with an autosampler and captured onto a reverse phase C4 analytical column for desalting using a water, 0.2% formic acid mobile phase.
  • the proteins are bumped from the C4 column using a 10%/90% water/acetonitrile pulse (both with 0.2% formic acid) and injected into an Agilent 6210 time-of-flight liquid chromatography/mass spectrometry system molecular weight analyser .
  • Theoretical mass-averaged molecular weights of the light chain and heavy chain components are determined using the GPMaw program (v. 8.20).
  • the two separate light chains of the competition experiment can be easily discriminated from one another based on their different molecular weights.
  • the relative counts of the ionized light chains hitting the detector are used to quantify the ratio of designed C L and WT C L protein that is bound to the heavy chain component and this data is shown in Table 6. Table 6. Results of the competition LC specificity LC/MS assay.
  • Example 3 Designs to generate designed V H and V L domains that bind one another stronger than they bind WT V L or V H domains, respectively.
  • V H N L variable heavy chain/variable light chain modifications
  • V L position 1 and V H position 62 are first identified for modification.
  • V L position 1 is modified to the positively charged residue arginine (R) and
  • V H position 62 is modified to the negatively charged residue glutamic acid (E).
  • This combination of charge modifications is denoted Design A.
  • a second design modified V L position 38 and V H position 39 to generate a charge pair (V L_ Q38D and V H_ Q39K) at the site of the former hydrogen bonding interaction. This charge pair introduction is denoted Design B.
  • Design A, Design B, and a combination of Design A and B, denoted Design AB are introduced into the plasmids for the pertuzumab light chain and heavy chain plasmids for mammalian expression.
  • Plasmids containing Design 1.0+5.0 (with WT petuzumab V H and V L ) modifications are also constructed to generate heavy chains and light chains to potentially improve specificity of the variable domain designs over pairing with fully wild type heavy and light chains .
  • the mutations are introduced using the using the QuikChange II mutagenesis kit (Agilent) according to the manufacturer's protocols constructs. The methods followed for plasmid production and purification are essentially as described in Example 1.
  • Each of the designed heavy chain and light chain plasmids are co-expressed transiently in HEK293F essentially as described in Example 1 .
  • the designed heavy chains and light chains are also expressed with a mismatched light chain or heavy chain as a control to probe for specificity.
  • the mismatched heavy chain and light chain contain WT V H and V L domains and the Design 1.0+5.0 in the constant domains to add additional specificity (denoted in Table 8 below as HC(WT15) and LC(WT15), respectively).
  • the expression supernatants are subjected to a thermal challenge by incubation for 1 hr at temperatures ranging from 45-75 °C and tested for binding hHER-2-Fc using an ELISA (methods described in Example 1 ).
  • This ELISA format is sensitive to the stability of the variable domains.
  • all proteins are purified from their supernatants using the protein G magnetic bead protocol, essentially as described in Example 1, and formed fully assembled IgG molecules. In each of the cases (Design A and Design B), the apparent thermal stability of the matched heavy chain and light chain pairs iss significantly higher than the mismatched pairs.
  • thermodynamically favored over the mismatched pairs provides a thermodynamic basis for the specific association of the Design A heavy chain and light chain for themselves and the Design B heavy chain and light chain for themselves over the association with the heavy chain and light chains containing WT variable domains.
  • Combining the designs into a single construct, Design AB further improved the thermodynamic specificity and resulted in reduced expression of the mismatched pairs. Results for the thermo-challenge testing are provided in Table 8. Table 8. Summary of the thermochallenge data with Design A, Design B, and Design AB.
  • Example 4 Multi-state computational designs to create additional V H /V L interface modifications that discriminate from the native immunoglobulin V H /V L interface.
  • Example 5 Combining the C H 1/C L and V H /V L interface designs results in highly specific HC/LC pairing.
  • variable domain Designs H.4, H.6 and AB are examined along with the constant domain Designs 2.1.3.2 and 2.1.3.3a.
  • the specificity afforded by the V H /V L and C H 1/C L designs in isolation and in combination with each other is measured using a similar LC/MS competition experiment as described in Example 3 (with the IgG/C L proteins lacking variable domains), but here full-length immunoglobulin heavy chains and light chains are used.
  • two full-length light chains (with V L and C L ) are co-expressed and forced to compete for binding to a single heavy chain prior to secretion.
  • Identities of the designs and the corresponding SEQ ID numbers for the constructs used in the specificity experiments are provided in Table 10.
  • 'AB+2133a HC' is a HC with Design AB in its V H and Design 2.1.3.3a in its C H1 .
  • the LC/MS specificity data for the combinations tested is provided in Table 11. Table 11. LC/MS analysis of the V H /V L and C H 1/C L interface designs in isolation and in combination.
  • BsAbs Two sets of IgG bispecific antibodies (BsAbs) are constructed to test how combining the designs AB2133a and H.4WT may enable specific heavy chain/light chain assembly of specific Fabs. All subcloning and mutagenesis protocols followed are essentially as described in previous Examples.
  • the first BsAb consists of a combination of pertuzumab (anti-HER-2) and matuzumab (anti-EGFR) ( see , Bier et al. (1998), Cancer Immunol. Immunother. 46; 167-173 ) and the second consists of a combination of MetMAb (anti-cMET) ( see, Jin et al. (2008), Cancer Res.
  • aspartic acid 399 and glutamic acid 356 are both mutated to lysine in one of the heavy chains of the anti-HER-2/anti-EGFR pair and one of the heavy chains of the anti-MET/anti-Axl pair.
  • the remaining heavy chain in each pair had lysine 409 and lysine 392 mutated to aspartic acid ( see, Gunasekaran et al. (2010), JBC 285; 19637-19646 ).
  • sequence ID numbers of the immunoglobulin chains used to generate the IgG BsAbs are provided in Table 12. Table 12.
  • Both the (+) and (-) -containing HCs also have the N297Q mutation to eliminate N-linked glycosylation.
  • b Nomenclature is essentially as described in Table 10 above. The first two characters of each protein specify the variable domain design, while the subsequent numbering specifies the constant domain design (e.g., a LC designated 'AB+2133a[p ⁇ ]' contains Design AB in its V L and Design 2.1.3.3a in its lambda C L . Similarly, an HC designated 'AB+2133a(-)[pG1]' contains Design AB in its V H and Design 2.1.3.3a in its C H1.
  • brackets refers to the variable and constant domain of the particular parental antibody HC or LC containing the indicated design (e.g., "[pG1]” refers to a heavy chain containing a pertuzumab variable domain and IgG1 constant domain, whereas "[mG1]” refers to a heavy chain with a matuzumab variable domain and IgG1 constant domain; similarly, “[p ⁇ ] refers to a light chain with pertuzumab variable domain and ⁇ constant domain, whereas "[MET ⁇ ]” refers to a light chain with METMAb variable domain and ⁇ constant domain)
  • V H /V L (AB and H.4) and C H 1/C L (2.1.3.3a and WT lamda or kappa) interfaces would enable specific IgG BsAb assembly over what occurs naturally with no FAb interface designs in place
  • transient transfections of particular designed Fab constructs followed by LC/MS analyses are performed.
  • IgG BsAb two heavy chains and two light chains are simultaneously transfected using separate plasmids into mammalian HEK293F cells using transfection protocols essentially as described in the previous Examples.
  • the designed IgG BsAbs include the deglycosylation mutation and Fc heterodimerization mutations as described above.
  • a control set of IgG BsAbs with the deglycosylation and Fc heterodimerization mutations and light chains with both C ⁇ or C ⁇ domains, but without the designed V H /V L and C H 1/C L modifications, are also created by transfection of appropriate heavy chains and light chains.
  • each Designed IgG BsAb pair one heavy chain and light chain (shown viable in both the C ⁇ and C ⁇ isotype) contained Design H.4, while the other heavy chain and light chain (shown viable in both the C ⁇ and C ⁇ isotype) contained Design AB and Design 2.1.3.3a.
  • the exact heavy chain and light chain composition of each IgG BsAb synthesized is provided in Table 13. Table 13.
  • the percent values represent the relative counts detected for covalently linked (non-reduced) heterotetramers HC1HC2LC1LC2 (correctly formed) compared to incorrect HC1HC2LC1LC1 (incorr.) and incorrect HC1HC2LC2LC2 (incorr.).
  • Each BsAb is designated ⁇ , ⁇ , ⁇ , or ⁇ based on the C L compositions (lambda or kappa) of its LCs.
  • Nomenclature for each heavy chain or light chain construct is essentially as described above in Tables 10 and 12
  • the IgG BsAbs may be tested for their oligomeric nature using analytical size exclusion chromatography (SEC).
  • SEC analytical size exclusion chromatography
  • the IgG BsAbs are purified at the 1 mL scale from HEK293F supernatants using the protein G magnetic bead procedure, essentially as described in Example 1.
  • SEC analysis between 10-50 ⁇ g of each protein was applied to a Yarra G3000 (7.8 ⁇ 300 mm) analytical SEC column (Phenomenex) with all other assay parameters similar to the protocol as described in Example 1 .
  • the anti-cMet/anti-Axl IgG BsAbs also demonstrate primarily monomeric behavior with retention times approximating the average of the control antibodies, non-bispecific antibodies.
  • the four anti-cMet/anti-Axl BsAbs containing the Fab specificity designs did not demonstrate this behavior.
  • the dual-binding behavior of the synthesized BsAbs may be assessed using both sandwich ELISA and surface plasmon resonance assays as follows.
  • Two sandwich ELISAs are developed, one for detecting anti-HER-2/anti-EGFR BsAb activity and one for detecting anti-cMET/anti-Axl BsAb activity.
  • clear 96-well round bottom high binding Immulon microtiter plates (Greiner bio-one, cat#650061) are coated overnight at 2-8 °C with 50 ⁇ L/well 1 ⁇ g/mL hHER-2-Fc or 1 ⁇ g/mL hHGFR(cMet)-Fc (both from R&D systems) in a 50 mM Na 2 CO 3 pH 8 buffer.
  • the plates are washed 4 times with PBST and blocked with 100 ⁇ L/well casein buffer (Pierce) for 1 hr at 37 °C.
  • the plates are then washed 4 times with PBST and the parental IgG controls or BsAb IgG test articles are added at 50 ⁇ L/well and 5 ⁇ g/mL and serially diluted 1:3 down the plate.
  • the test articles are incubated on the plate for 1 hr at 37 °C.
  • the plates are then washed 4 times with PBST and 50 ⁇ L/ well 0.2 ⁇ g/mL hEGFR-Fc-biotin or hAxl-Fc-biotin (both from R&D systems) is added for 1 hr at 37 °C.
  • the plates are then washed 4 times with PBST followed by the addition of a 50 ⁇ L/well streptavidin-HRP (Jackson Labs) diluted 1:2000 in PBST.
  • the streptavidin-HRP is incubated in each well for 1 hr at 37 °C.
  • the plates are then washed 4 times with PBST and 100 ⁇ L/well 1-component TMB substrate is added (KPL laboratories). After approximately 10 minutes, 100 mL/well 1% H 3 P0 4 (in H 2 O) is added to each plate to quench the reaction.
  • Absorbance (450 nm) of every well in the plates is read using a SpectraMax UV plate reader (Molecular Devices). Biotin-labeling of the hEGFR-Fc and hAxl-Fc proteins is performed using EZ-Link Sulfo-NHS-LC-Biotin (Thermo Scientific) according to the manufacturer's protocol.
  • Both sandwich ELISAs were capable of demonstrating the dual-binding behavior of the BsAbs.
  • the monoclonal IgG controls (pG1, mG1, METG1, or AxlG1) demonstrated no ability to generate signal in the sandwich ELISAs.
  • the control IgG BsAbs with no Fab redesigns (HEControl ⁇ , HEControl ⁇ , MAControl ⁇ , MAControl ⁇ ) generated sigmoidal binding curves in the assay. All the IgG BsAbs with the Fab redesigns also demonstrated sigmoidal binding curves.
  • HEControl EC 50 470 ⁇ 90 ng/mL
  • HEDesign EC 50 280 ⁇ 20 ng/mL
  • MAControl EC 50 260 ⁇ 80
  • MADesign EC 50 220 ⁇ 20.
  • hHER-2-Fc-biotin and hAxl-Fc-biotin are immobilized onto SA sensorchip surfaces by injection of 20 ⁇ L over 2 minutes at 10 ⁇ L/min.
  • each control IgG, control IgG BsAb, or designed IgG BsAb is injected over these sensorchip surfaces at 5 ⁇ L/min followed by a secondary 20 ⁇ L injection of 20 nM hEGFR-Fc or hHGFR(cMet)-Fc.
  • the hHER-2-Fc and hAxl-Fc sensorchip surfaces are regenerated by raising the flow rate to 50 ⁇ L/min and injecting two 5 ⁇ L injections of a 0.1 M glycine solution at pH 2.5 and pH 2.0, respectively.
  • constant domain (C H 1/C L ) design denoted 2133a was determined to provide less correct HC/LC pairing specificity when used in C H 1/C ⁇ compared to its use in C H 1/C ⁇ (See, for example the EGFRxHER2 bispecific antibody assembly in Table 13 ). It was also found that the 2133a constant domain design destabilized when used in C H 1/C ⁇ compared to WT C H 1/C ⁇ (see Table 15, below).
  • the T m of the 2133a-containing C H 1/C ⁇ domain was 67.7 °C while that of WT C H 1/C ⁇ was 70.8 °C.
  • DSC is performed using an automated capillary DSC (capDSC, GE Healthcare). Protein solutions and reference (buffer) solutions are sampled automatically from a 96-well plate using the robotic attachment. Before each protein scan, at least one buffer/buffer scan is performed to define the baseline for subtraction. All 96-well plates containing protein are stored within the instrument at 6_°C. Samples are run at 1.0 mg/ml protein concentration in PBS. Scans are performed from 10 to 95_°C at 90_°C/hr using the low feedback mode. Scans are analyzed using the Origin software supplied by the manufacturer.
  • nonzero protein scan baselines are corrected using a third-order polynomial. Based on the analyses, the IgG1/ C ⁇ protein harboring the 2133a design was less stable than the WT protein (see Table 15, below).
  • C H 1_A172 design 2133a already contains an H172A substitution
  • C H 1_V190 residue positions to randomize.
  • the 2133a IgG1/ C ⁇ constructs lacking variable domains are used to create the libraries for screening and analysis.
  • the libraries are generated using the QuikChange II Site-Directed Mutagenesis Kit (Agilent) using protocols provided by the manufacturer.
  • the constructs are expressed via transient transfection in HEK293F cells as generally described in Example 1. Titers of the proteins are assessed using the HPLC Protein G quantitation and collection method as generally described in Example 2.
  • the proteins are assessed for their stability properties using a thermal challenge assay similar to that described in Example 1.
  • the plates are coated with a sheep anti-human Fd (CHI) polyclonal antibody (Meridian Life Sciences, cat#W90075C) at 1 ⁇ g/mL and 100 ⁇ L/well in a 0.05 M NaHCO 3 buffer, pH 8.3 for 1 hr at 37 °C or overnight at 4 °C.
  • CHI sheep anti-human Fd
  • Thermally resistant IgG1/ C ⁇ protein is detected by adding a detection antibody (HRP-labeled goat anti-human kappa, Southern Biotechnology, cat#2060-5) at a 1:10,000 dilution in PBS-T into every well at 100 ⁇ L/well and incubating for 1 hr at 37 °C.
  • detection antibody HRP-labeled goat anti-human kappa, Southern Biotechnology, cat#2060-5
  • Modified 2133a HC for Improved Stability Sequence ID number HC (-V H ) 2133a_A172R SEQ ID 65 HC (-V H ) 2133a_V190M SEQ ID 66 HC (-V H ) 2133a_V190I SEQ ID 67 HC (-V H ) 2133a_A172R_V190M SEQ ID 68 HC (-V H ) 2133a_ A172R_V190I SEQ ID 69 C ⁇ _2133a_V133L SEQ ID 70 C ⁇ _2133a_S174Q SEQ ID 71 C ⁇ _2133a_S174D SEQ ID 72 C ⁇ _2133a_V133L_S174Q SEQ ID 73 C ⁇ _2133a_V133L_S174D SEQ ID 74 (-)PG1_AB2133a a SEQ ID 13 (-)
  • Both the (+) and (-) -containing HCs also have the N297Q mutation to eliminate N-linked glycosylation.
  • b 'MR' refers to C H 1 mutations A172R and V190M.
  • 'IR' refers to C H 1 mutations A172R and V190I.
  • 'LD' refers to C ⁇ mutations V133L and S174D.
  • 'LQ' refers to C ⁇ mutations V133L and S174Q.
  • Table 15 Expression and differential scanning calorimetry (DSC) results for mutants of the 2133a-containing IgG1/C ⁇ protein lacking variable domains.
  • DSC T m (°C) a HC (-V H ) WT/C ⁇ _WT 15 70.8 ⁇ 0.1 HC (-V H ) 2133a/C ⁇ _2133a 19 67.7 ⁇ 0.2 HC (-V H ) 2133a_A172R/C ⁇ _2133a 16 70.0 HC (-V H ) 2133a_V190M/C ⁇ _2133a 21 69.1 HC (-V H ) 2133a_V190I/C ⁇ _2133a 14 68.6 HC (-V H ) 2133a_A172R_V190M/C ⁇ _2133a 43 70.1 HC (-V H ) 2133a_A172R_V190I/C ⁇ _2133a 43 69.2 a
  • the DSC Tm refers to the midpoint of the cooperative unfolding transition of the C H 1/C ⁇ heterodimer in each of these constructs.
  • the specificity afforded by the 2133a design mutations in C H 1/C ⁇ instead of C H 1/C ⁇ is assessed.
  • the WT C ⁇ protein shows little tendency to associate with the 2133a HC (SEQ ID 18) protein with or without the stabilizing mutations depicted in Table 15.
  • the 2133a-containing CK domain SEQ ID 64
  • the 2133a-containing CK domain could associate with a WT HC (SEQ ID 3) more strongly than a WT CK domain (SEQ ID 63, see Table 16, below).
  • 2133a CK residue positions V133 and S174 were identified as positions where potential new interactions with 2133a-containing C H 1 domains could be generated, that might be incompatible with WT C H 1.
  • Screening for 2133a CK mutations that maintained binding to the 2133a design HC, while decreasing binding with WT HC, three mutations (C ⁇ _ V133L, C ⁇ _ S174Q, and C ⁇ _ S174D) were found to provide beneficial specificity in the LC CK competition assay (Table 16) (Sequence ID numbers of these constructs are provided in Table 14, above).
  • the 2133a C H 1 and C ⁇ mutants were then added to two separate full-length HCs and LCs (including variable domains) to assess their ability to impact specific bispecific antibody assembly.
  • the 2133a C H 1 mutants A172R and V190M (denoted 'MR') and A172R and V190I (denoted 'IR') were each combined for the testing as were the compatible design 2133a C ⁇ mutants V133L and S174D (denoted 'LD') and V133L and S174Q (denoted 'LQ').
  • the mutants were added to both a Pertuzumab (anti-HER2) and MetMAb (anti-cMet) IgG1/kappa HC/LC pair containing the 2133a designs.
  • the Pertuzumab and MetMAb HCs contained the K409D and K392D mutations, denoted '(-)', while the complementary Matuzumab and Trastuzumab HCs contained the D399K and E356K mutations, denoted '(+)' ( see , Gunasekaran et al., (2010), JBC 285; 19637-19646 ). Both the (+) and (-) - containing HCs also have the N297Q mutation to eliminate N-linked glycosylation.
  • the Pertuzumab HC/LC pairs were co-expressed with an H4WT-containing Matuzumab IgG1/kappa HC/LC pair to form a HER2 ⁇ EGFR IgG bispecific antibody.
  • the MetMAb HC/LC pairs were co-expressed with an H4WT-containing Trastuzumab IgG1/kappa HC/LC pair to form a cMet ⁇ HER2 IgG bispecific antibody.
  • the Sequence ID numbers for all sequences used in the study are provided in Table 14, above. All LCs in this study were fully kappa (i.e., VKCK).
  • Both the 'LD' and 'LQ' paired mutations provided significant improvements in correct LC pairing within the IgG bispecific antibodies over utilization of unmodified AB2133a kappa LCs.
  • Adding 'LD' and 'LQ' mutant combinations to the AB2133a C ⁇ provided an average 13% and 12%, respectively, benefit in correct LC assembly over what was obtained in their absence.
  • the HC 'MR' and 'IR' mutations are stabilizing to the 2133a C H 1/ C ⁇ interaction, their impact on specificity was less clear. Adding the HC 'MR' and 'IR' mutations in isolation decreased the correct IgG bispecific antibody assembly in all cases.
  • variable domains that drive improved HC/LC pairing specificity were pursued.
  • a charge/polar pair of amino acids at HC_Q105/LC_K42 was identified for manipulation.
  • LC_K42 was mutated to D and HC_Q105 was mutated to R within the pertuzumab IgG1/kappa H4WT design.
  • LC_K42D and HC_Q105R when added to H4 variable domain designs, provided slight improvement in H4(+ K42D) pertuzumab LC pairing with its cognate HC H4(+Q105R) design when co-expressed with an AB2133a pertuzumab LC ( ⁇ 20% improvement).
  • Co-expressing the H4(+K42D) pertuzumab LC with the design AB2133a pertuzumab LC and HC also did not markedly decrease the observed assembly level of the design AB2133a pertuzumab HC and LC pair.
  • This additional design mutation (HC_Q105R/LC_K42D) is denoted as 'DR' in the Tables 18 and 19 below.
  • Pertuzumab with H4WT IgG1/kappa was tested for bispecific IgG assembly with Trastuzumab-containing the AB2133a designs in IgG1/kappa.
  • the Pertuzumab and Trastuzumab HCs containing the AB2133a Fab designs contained the K409D and K392D mutations, denoted '(-)', while the complementary H4WT designs (with and without the 'DR' and/or 'CS' mutations) contained the D399K and E356K mutations, denoted '(+)' ( see , Gunasekaran et al., (2010), JBC 285; 19637-19646 ). Both the (+) and (-) - containing HCs also had the N297Q mutation to eliminate N-linked glycosylation.
  • the HC and LC from Pertuzumab are co-transfected with the HC and LC of a second antibody in 2 mL HEK293F cells.
  • the resulting material is secreted from the cells, purified as described in Example 2 and characterized by MS.
  • the Sequence ID numbers of all the HCs and LCs used in the experiment are provided in Table 18 .
  • Table 18 Sequence ID numbers of the HC and LC designs improving the specificity of HC/LC assembly.
  • Example 8 and Example 9 can be utilized to improve the HC/LC pairing stability and specificity within IgG bispecific antibodies. This was particularly evident when both LCs of the IgG bispecific antibody were fully kappa; a scenario where the AB2133a designs provide less specificity than when the AB2133a designs are used within a V ⁇ C ⁇ LC.

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Claims (17)

  1. Verfahren zur Produktion eines ersten und eines zweiten antigenbindenden Fragments (Fab), umfassend:
    (1) Koexprimieren einer ersten Nukleinsäure, einer zweiten Nukleinsäure, einer dritten Nukleinsäure und einer vierten Nukleinsäure in einer Wirtszelle, wobei:
    (a) die erste Nukleinsäure sowohl eine variable Domäne einer ersten schweren Kette als auch eine konstante CH1 -Domäne einer ersten schweren Kette von IgG kodiert, wobei die variable Domäne der ersten schweren Kette ein Lysin an Rest 39 und eine Glutaminsäure an dem Rest, der vier Aminosäuren stromaufwärts von dem ersten Rest von HFR3 gemäß Kabat ist, umfasst und die konstante CH1 -Domäne der ersten schweren Kette von IgG ein Alanin oder Arginin an Rest 172 und ein Glycin an Rest 174 umfasst;
    (b) die zweite Nukleinsäure sowohl eine variable Domäne einer ersten leichten Kette und eine konstante Domäne der ersten leichten Kette kodiert, wobei die variable Domäne der ersten leichten Kette ein Kappa-Isotyp ist und ein Arginin an Rest 1 und eine Asparaginsäure an Rest 38 umfasst und die konstante Domäne der ersten leichten Kette ein Tyrosin an Rest 135 und ein Tryptophan an Rest 176 umfasst;
    (c) die dritte Nukleinsäure sowohl eine variable Domäne einer zweiten schweren Kette und eine konstante CH1-Domäne einer zweiten schweren Kette von IgG kodiert, wobei die variable Domäne der zweiten schweren Kette ein Tyrosin an Rest 39 umfasst und die konstante CH1-Domäne der zweiten schweren Kette von IgG eine WT-Sequenz umfasst, und die vierte Nukleinsäure sowohl eine variable Domäne einer zweiten leichten Kette als auch eine konstante Domäne der zweiten leichten Kette kodiert, wobei die variable Domäne der zweiten leichten Kette ein Arginin an Rest 38 umfasst und die konstante Domäne der zweiten leichten Kette eine WT-Sequenz umfasst; oder
    (d) die dritte Nukleinsäure sowohl eine variable Domäne einer zweiten schweren Kette und eine konstante CH1-Domäne einer zweiten schweren Kette von IgG kodiert, wobei die variable Domäne der zweiten schweren Kette ein Tyrosin an Rest 39 umfasst und die konstante CH1-Domäne der zweiten schweren Kette von IgG eine Asparaginsäure an Rest 228 umfasst, und die vierte Nukleinsäure sowohl eine variable Domäne einer zweiten leichten Kette als auch eine konstante Domäne der zweiten leichten Kette kodiert, wobei die variable Domäne der zweiten leichten Kette ein Arginin an Rest 38 umfasst und die konstante Domäne der zweiten leichten Kette ein Lysin an Rest 122 umfasst;
    wobei jede von den variablen Domänen der ersten schweren Kette und der ersten leichten Kette drei komplementaritätsbestimmende Regionen (CDR) umfasst, die direkt an ein erstes Antigen binden, und weiterhin wobei jede von den variablen Domänen der zweiten schweren Kette und der zweiten leichten Kette drei komplementaritätsbestimmende Regionen (CDR) umfasst, die direkt an ein zweites Antigen binden, das sich von dem ersten Antigen unterscheidet;
    wobei die konstanten Domänen der ersten und der zweiten schweren Kette von IgG vom humanen IgG1- oder IgG4-Isotyp sind;
    (2) Kultivieren der Wirtszelle unter Bedingungen, so dass die variablen Domänen und die konstanten CH1-Domänen der ersten und der zweiten schweren Kette von IgG und die variablen und die konstanten Domänen der ersten und der zweiten leichten Kette produziert werden; und
    (3) Gewinnen eines ersten und eines zweiten Fab aus der Wirtszelle, wobei das erste Fab die variable und die konstante Domäne der ersten schweren Kette und die variable und die konstante Domäne der ersten leichten Kette umfasst und das zweite Fab die variable und die konstante Domäne der zweiten schweren Kette und die variable und die konstante Domäne der zweiten leichten Kette umfasst.
  2. Verfahren nach Anspruch 1, wobei die konstante CH1-Domäne der ersten schweren Kette von IgG weiterhin ein Methionin oder Isoleucin, das an Rest 190 substituiert ist, umfasst.
  3. Verfahren nach Anspruch 1 oder 2, wobei die konstante Domäne der ersten leichten Kette ein Kappa-Isotyp ist und weiterhin ein Leucin, das an Rest 133 substituiert ist, umfasst.
  4. Verfahren nach einem der Ansprüche 2-3, wobei die konstante Domäne der ersten leichten Kette ein Kappa-Isotyp ist und weiterhin ein Glutamin oder eine Asparaginsäure, das bzw. die an Rest 174 substituiert ist, umfasst.
  5. Verfahren nach einem der Ansprüche 1-4, wobei die variable Domäne der zweiten schweren Kette weiterhin ein Arginin, das an Rest 105 subsituiert ist, umfasst und die variable Domäne der zweiten leichten Kette weiterhin eine Asparaginsäure, die an Rest 42 substituiert ist, umfasst.
  6. Verfahren nach einem der Ansprüche 1-6, wobei die Wirtszelle eine Säugetierzelle ist.
  7. Verfahren nach einem der Ansprüche 1-7, wobei die konstanten Domänen der ersten und der zweiten leichten Kette vom Kappa-Isotyp sind.
  8. Verfahren zur Produktion eines bispezifischen Antikörpers, umfassend:
    (1) Koexprimieren einer ersten Nukleinsäure, einer zweiten Nukleinsäure, einer dritten Nukleinsäure und einer vierten Nukleinsäure in einer Wirtszelle, wobei:
    (a) die erste Nukleinsäure eine erste schwere Kette von IgG kodiert, wobei die erste schwere Kette eine variable Domäne, die ein Lysin, das an Rest 39 substituiert ist, und eine Glutaminsäure an dem Rest, der vier Aminosäuren stromaufwärts von dem ersten Rest von HFR3 gemäß Kabat ist, umfasst, und eine konstante CH1-Domäne, die ein Alanin oder Arginin an Rest 172 und ein Glycin an Rest 174 umfasst, umfasst;
    (b) die zweite Nukleinsäure eine erste leichte Kette kodiert, wobei die leichte Kette eine variable Kappa-Domäne, die ein Arginin an Rest 1 und eine Asparaginsäure an Rest 38 umfasst, und eine konstante Domäne, die ein Tyrosin an Rest 135 und ein Tryptophan an Rest 176 umfasst, umfasst;
    (c) die dritte Nukleinsäure eine zweite schwere Kette von IgG kodiert, wobei die zweite schwere Kette eine variable Domäne, die ein Tyrosin an Rest 39 umfasst, und eine konstante CH1-Domäne, die eine WT-Sequenz umfasst, umfasst, und die vierte Nukleinsäure eine zweite leichte Kette kodiert, wobei die zweite leichte Kette eine variable Domäne, die ein Arginin an Rest 38 umfasst, und eine konstante Domäne, die eine WT-Sequenz umfasst, umfasst; oder
    (d) die dritte Nukleinsäure eine zweite schwere Kette von IgG kodiert, wobei die zweite schwere Kette eine variable Domäne, die ein Tyrosin an Rest 39 umfasst, und eine konstante CH1-Domäne, die eine Asparaginsäure an Rest 228 umfasst, umfasst, und die vierte Nukleinsäure eine zweite leichte Kette kodiert, wobei die zweite leichte Kette eine variable Domäne, die ein Arginin an Rest 38 umfasst, und eine konstante Domäne, die ein Lysin an Rest 122 umfasst, umfasst, wobei jede von den variablen Domänen der ersten schweren Kette und der ersten leichten Kette drei komplementaritätsbestimmende Regionen (CDR) umfasst, die direkt an ein erstes Antigen binden, und weiterhin wobei jede von den variablen Domänen der zweiten schweren Kette und der zweiten leichten Kette drei komplementaritätsbestimmende Regionen (CDR) umfasst, die direkt an ein zweites Antigen binden, das sich von dem ersten Antigen unterscheidet; und wobei die konstanten Domänen der ersten und der zweiten schweren Kette von IgG vom humanen IgG1- oder IgG4-Isotyp sind;
    (2) Kultivieren der Wirtszelle unter Bedingungen, so dass die erste und die zweite schwere Kette von IgG und die erste und die zweite leichte Kette produziert werden; und
    (3) Gewinnen eines bispezifischen Antikörpers aus der Wirtszelle, der ein erstes und ein zweites antigenbindendes Fragment (Fab) umfasst, wobei das erste Fab die erste schwere Kette von IgG und die erste leichte Kette umfasst und das zweite Fab die zweite schwere Kette von IgG und die zweite leichte Kette umfasst.
  9. Verfahren nach Anspruch 8, wobei die konstante CH1-Domäne der ersten schweren Kette von IgG weiterhin ein Methionin oder Isoleucin an Rest 190 umfasst.
  10. Verfahren nach Anspruch 8 oder 9, wobei die konstante Domäne der ersten leichten Kette ein Kappa-Isotyp ist und weiterhin ein Leucin an Rest 133 umfasst.
  11. Verfahren nach einem der Ansprüche 8-10, wobei die konstante Domäne der ersten leichten Kette ein Kappa-Isotyp ist und weiterhin ein Glutamin oder eine Asparaginsäure an Rest 174 umfasst.
  12. Verfahren nach einem der Ansprüche 8-11, wobei die variable Domäne der zweiten schweren Kette weiterhin ein Arginin an Rest 105 umfasst und die variable Domäne der zweiten leichten Kette weiterhin eine Asparaginsäure an Rest 42 umfasst.
  13. Verfahren nach einem der Ansprüche 8 bis 12, wobei eine von der ersten und der zweiten schweren Kette von IgG weiterhin eine konstante CH3-Domäne umfasst, die ein Lysin an Rest 356 und ein Lysin an Rest 399 umfasst, und die andere von der ersten und der zweiten schweren Kette von IgG weiterhin eine konstante CH3-Domäne umfasst, die eine Asparaginsäure an Rest 392 und eine Asparaginsäure an Rest 409 umfasst.
  14. Verfahren nach einem der Ansprüche 8-13, wobei die Wirtszelle eine Säugetierzelle ist.
  15. Verfahren nach einem der Ansprüche 8-14, wobei die konstanten Domänen der ersten und der zweiten leichten Kette vom Kappa-Isotyp sind.
  16. Antigenbindendes Fragment (Fab), das nach einem der Ansprüche 1-7 produziert wird.
  17. Bispezifischer Antikörper, der nach einem der Ansprüche 8-15 produziert wird.
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